Mercurial > repos > peterjc > blastxml_to_top_descr
annotate tools/ncbi_blast_plus/blastxml_to_top_descr.xml @ 7:a7add03a44fd draft
Uploaded v0.0.6, checks return code for error handling
author | peterjc |
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date | Wed, 17 Apr 2013 11:46:03 -0400 |
parents | 8a0771c5e236 |
children | a8ef75aab1f9 |
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Uploaded v0.0.6, checks return code for error handling
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1 <tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.6"> |
0 | 2 <description>Make a table from BLAST XML</description> |
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8a0771c5e236
Uploaded v0.0.5, reports number of queries with hits in stdout (peek text).
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3 <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> |
0 | 4 <command interpreter="python"> |
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Uploaded v0.0.4, quotes filenames in case the contain spaces
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5 blastxml_to_top_descr.py "${blastxml_file}" "${tabular_file}" ${topN} |
0 | 6 </command> |
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Uploaded v0.0.6, checks return code for error handling
peterjc
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7 <stdio> |
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Uploaded v0.0.6, checks return code for error handling
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8 <!-- Assume anything other than zero is an error --> |
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Uploaded v0.0.6, checks return code for error handling
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9 <exit_code range="1:" /> |
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Uploaded v0.0.6, checks return code for error handling
peterjc
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10 <exit_code range=":-1" /> |
a7add03a44fd
Uploaded v0.0.6, checks return code for error handling
peterjc
parents:
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11 </stdio> |
0 | 12 <inputs> |
13 <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> | |
14 <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/> | |
15 </inputs> | |
16 <outputs> | |
17 <data name="tabular_file" format="tabular" label="Top $topN descriptions from $blastxml_file.name" /> | |
18 </outputs> | |
19 <requirements> | |
20 </requirements> | |
21 <tests> | |
22 <test> | |
23 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> | |
24 <param name="topN" value="3" /> | |
25 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3.tabular" ftype="tabular" /> | |
26 </test> | |
27 </tests> | |
28 <help> | |
29 | |
30 **What it does** | |
31 | |
32 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of | |
33 formats including text, tabular and a more detailed XML format. You can | |
34 do a lot of things with tabular files in Galaxy (sorting, filtering, joins, | |
35 etc) however currently the BLAST tabular output omits the hit descriptions | |
36 found in the other output formats. | |
37 | |
38 This tool turns a BLAST XML file into a simple tabular file containing | |
39 one row per query sequence, containing the query identifier and then | |
40 the three (by default) top hit descriptions. If a query doesn't have | |
41 that many hits, then these entries are left blank. | |
42 | |
43 **Example Usage** | |
44 | |
45 One simple usage would be to take a transcriptome assembly or set of | |
46 gene predictions, run a BLAST search against the NCBI NR database, and | |
47 then use this tool to make a table of the top three BLAST hits. This | |
48 can give you a 'quick and dirty' crude annotation, potentially enough | |
49 to spot some problems (e.g. bacterial contaimination could be very | |
50 obvious). | |
51 | |
52 </help> | |
53 </tool> |